Merge branch 'trixi-framework:main' into main

.JuliaFormatter.toml

@@ -0,0 +1,8 @@
+# Use SciML style: https://github.com/SciML/SciMLStyle
+style = "sciml"
+
+# Python style alignment. See https://github.com/domluna/JuliaFormatter.jl/pull/732.
+yas_style_nesting = true
+
+# Align struct fields for better readability of large struct definitions
+align_struct_field = true

.github/workflows/Documenter.yml

@@ -36,7 +36,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.8'
+          version: '1.9'
           show-versioninfo: true
       - uses: julia-actions/julia-buildpkg@v1
         env:

.github/workflows/FormatCheck.yml

@@ -0,0 +1,44 @@
+name: format-check
+
+on:
+  push:
+    branches:
+      - 'main'
+    tags: '*'
+  pull_request:
+
+jobs:
+  check-format:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v3
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version = "0.13.0"))'
+        #
+        # TODO: Change the call below to
+        #       format(".")
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(["benchmark", "ext", "src", "utils"])'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v3
       - name: Check spelling
-        uses: crate-ci/[email protected].9
+        uses: crate-ci/[email protected].12

.github/workflows/benchmark.yml

@@ -11,7 +11,7 @@ jobs:
         os:
           - ubuntu-latest
         version:
-          - '1.8'
+          - '1.9'
         arch:
           - x64
     steps:

.github/workflows/ci.yml

@@ -52,7 +52,8 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.8'
+          - '1.9'
+          # - '~1.9.0-0' # including development versions
           # - 'nightly'
         os:
           - ubuntu-latest
@@ -79,18 +80,22 @@ jobs:
           - threaded
         include:
           - version: '1.8'
+            os: ubuntu-latest
+            arch: x64
+            trixi_test: threaded_legacy
+          - version: '1.9'
             os: macOS-latest
             arch: x64
             trixi_test: mpi
-          - version: '1.8'
+          - version: '1.9'
             os: macOS-latest
             arch: x64
             trixi_test: threaded
-          - version: '1.8'
+          - version: '1.9'
             os: windows-latest
             arch: x64
             trixi_test: mpi
-          - version: '1.8'
+          - version: '1.9'
             os: windows-latest
             arch: x64
             trixi_test: threaded
@@ -121,7 +126,7 @@ jobs:
           TRIXI_TEST: ${{ matrix.trixi_test }}
       - uses: julia-actions/julia-processcoverage@v1
         with:
-          directories: src,examples
+          directories: src,examples,ext
       - uses: codecov/codecov-action@v3
         with:
           file: ./lcov.info

Project.toml

@@ -1,7 +1,7 @@
 name = "Trixi"
 uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
 authors = ["Michael Schlottke-Lakemper <[email protected]>", "Gregor Gassner <[email protected]>", "Hendrik Ranocha <[email protected]>", "Andrew R. Winters <[email protected]>", "Jesse Chan <[email protected]>"]
-version = "0.5.25-pre"
+version = "0.5.29-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
@@ -42,6 +42,12 @@ Triangulate = "f7e6ffb2-c36d-4f8f-a77e-16e897189344"
 TriplotBase = "981d1d27-644d-49a2-9326-4793e63143c3"
 TriplotRecipes = "808ab39a-a642-4abf-81ff-4cb34ebbffa3"
 
+[weakdeps]
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+
+[extensions]
+TrixiMakieExt = "Makie"
+
 [compat]
 CodeTracking = "1.0.5"
 ConstructionBase = "1.3"
@@ -53,6 +59,7 @@ HDF5 = "0.14, 0.15, 0.16"
 IfElse = "0.1"
 LinearMaps = "2.7, 3.0"
 LoopVectorization = "0.12.118"
+Makie = "0.19"
 MPI = "0.20"
 MuladdMacro = "0.2.2"
 Octavian = "0.3.5"
@@ -66,7 +73,7 @@ Requires = "1.1"
 SciMLBase = "1.90"
 Setfield = "0.8, 1"
 SimpleUnPack = "1.1"
-StartUpDG = "0.16"
+StartUpDG = "0.17"
 Static = "0.3, 0.4, 0.5, 0.6, 0.7, 0.8"
 StaticArrayInterface = "1.4"
 StaticArrays = "1"
@@ -78,3 +85,6 @@ Triangulate = "2.0"
 TriplotBase = "0.1"
 TriplotRecipes = "0.1"
 julia = "1.8"
+
+[extras]
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"

README.md

@@ -64,7 +64,7 @@ installation and postprocessing procedures. Its features include:
 ## Installation
 If you have not yet installed Julia, please [follow the instructions for your
 operating system](https://julialang.org/downloads/platform/). Trixi.jl works
-with Julia v1.8.
+with Julia v1.8 and newer. We recommend using the latest stable release of Julia.
 
 ### For users
 Trixi.jl and its related tools are registered Julia packages. Hence, you

benchmark/benchmark_ec.jl

@@ -1,50 +1,50 @@
 using Printf, BenchmarkTools, Trixi
 
-function run_benchmarks(benchmark_run; levels=0:5, polydeg=3)
-  runtimes = zeros(length(levels))
-  for (idx,initial_refinement_level) in enumerate(levels)
-    result = benchmark_run(; initial_refinement_level, polydeg)
-    display(result)
-    runtimes[idx] = result |> median |> time # in nanoseconds
-  end
-  return (; levels, runtimes, polydeg)
+function run_benchmarks(benchmark_run; levels = 0:5, polydeg = 3)
+    runtimes = zeros(length(levels))
+    for (idx, initial_refinement_level) in enumerate(levels)
+        result = benchmark_run(; initial_refinement_level, polydeg)
+        display(result)
+        runtimes[idx] = result |> median |> time # in nanoseconds
+    end
+    return (; levels, runtimes, polydeg)
 end
 
 function tabulate_benchmarks(args...; kwargs...)
-  result = run_benchmarks(args...; kwargs...)
-  println("#Elements | Runtime in seconds")
-  for (level,runtime) in zip(result.levels, result.runtimes)
-    @printf("%9d | %.2e\n", 4^level, 1.0e-9 * runtime)
-  end
-  for (level,runtime) in zip(result.levels, result.runtimes)
-    @printf("%.16e\n", 1.0e-9 * runtime)
-  end
+    result = run_benchmarks(args...; kwargs...)
+    println("#Elements | Runtime in seconds")
+    for (level, runtime) in zip(result.levels, result.runtimes)
+        @printf("%9d | %.2e\n", 4^level, 1.0e-9*runtime)
+    end
+    for (level, runtime) in zip(result.levels, result.runtimes)
+        @printf("%.16e\n", 1.0e-9*runtime)
+    end
 end
 
-function benchmark_euler(; initial_refinement_level=1, polydeg=3)
+function benchmark_euler(; initial_refinement_level = 1, polydeg = 3)
+    γ = 1.4
+    equations = CompressibleEulerEquations2D(γ)
 
-  γ = 1.4
-  equations = CompressibleEulerEquations2D(γ)
+    surface_flux = flux_ranocha
+    volume_flux = flux_ranocha
+    solver = DGSEM(polydeg, surface_flux, VolumeIntegralFluxDifferencing(volume_flux))
 
-  surface_flux = flux_ranocha
-  volume_flux  = flux_ranocha
-  solver = DGSEM(polydeg, surface_flux, VolumeIntegralFluxDifferencing(volume_flux))
+    coordinates_min = (-2.0, -2.0)
+    coordinates_max = (2.0, 2.0)
+    mesh = TreeMesh(coordinates_min, coordinates_max,
+                    initial_refinement_level = initial_refinement_level,
+                    n_cells_max = 100_000)
 
-  coordinates_min = (-2.0, -2.0)
-  coordinates_max = ( 2.0,  2.0)
-  mesh = TreeMesh(coordinates_min, coordinates_max,
-                  initial_refinement_level=initial_refinement_level,
-                  n_cells_max=100_000)
+    semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_weak_blast_wave,
+                                        solver)
 
-  semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_weak_blast_wave, solver)
+    t0 = 0.0
+    u0 = compute_coefficients(t0, semi)
+    du = similar(u0)
 
-  t0 = 0.0
-  u0 = compute_coefficients(t0, semi)
-  du = similar(u0)
-
-  @benchmark Trixi.rhs!($du, $u0, $semi, $t0)
+    @benchmark Trixi.rhs!($du, $u0, $semi, $t0)
 end
 
 # versioninfo(verbose=true)
 @show Threads.nthreads()
-tabulate_benchmarks(benchmark_euler, levels=0:8)
+tabulate_benchmarks(benchmark_euler, levels = 0:8)

benchmark/benchmarks.jl

@@ -1,3 +1,6 @@
+# Disable formatting this file since it contains highly unusual formatting for better
+# readability
+#! format: off
 
 using BenchmarkTools
 using Trixi

benchmark/elixir_2d_euler_vortex_p4est.jl

@@ -17,43 +17,42 @@ The classical isentropic vortex test case of
   [NASA/CR-97-206253](https://ntrs.nasa.gov/citations/19980007543)
 """
 function initial_condition_isentropic_vortex(x, t, equations::CompressibleEulerEquations2D)
-  # needs appropriate mesh size, e.g. [-10,-10]x[10,10]
-  # make sure that the inicenter does not exit the domain, e.g. T=10.0
-  # initial center of the vortex
-  inicenter = SVector(0.0, 0.0)
-  # size and strength of the vortex
-  iniamplitude = 0.2
-  # base flow
-  rho = 1.0
-  v1 = 1.0
-  v2 = 1.0
-  vel = SVector(v1, v2)
-  p = 10.0
-  rt = p / rho                  # ideal gas equation
-  cent = inicenter + vel*t      # advection of center
-  cent = x - cent               # distance to centerpoint
-  #cent=cross(iniaxis,cent)     # distance to axis, tangent vector, length r
-  # cross product with iniaxis = [0,0,1]
-  cent = SVector(-cent[2], cent[1])
-  r2 = cent[1]^2 + cent[2]^2
-  du = iniamplitude/(2*π)*exp(0.5*(1-r2)) # vel. perturbation
-  dtemp = -(equations.gamma-1)/(2*equations.gamma*rt)*du^2            # isentrop
-  rho = rho * (1+dtemp)^(1\(equations.gamma-1))
-  vel = vel + du*cent
-  v1, v2 = vel
-  p = p * (1+dtemp)^(equations.gamma/(equations.gamma-1))
-  prim = SVector(rho, v1, v2, p)
-  return prim2cons(prim, equations)
+    # needs appropriate mesh size, e.g. [-10,-10]x[10,10]
+    # make sure that the inicenter does not exit the domain, e.g. T=10.0
+    # initial center of the vortex
+    inicenter = SVector(0.0, 0.0)
+    # size and strength of the vortex
+    iniamplitude = 0.2
+    # base flow
+    rho = 1.0
+    v1 = 1.0
+    v2 = 1.0
+    vel = SVector(v1, v2)
+    p = 10.0
+    rt = p / rho                  # ideal gas equation
+    cent = inicenter + vel * t      # advection of center
+    cent = x - cent               # distance to centerpoint
+    #cent=cross(iniaxis,cent)     # distance to axis, tangent vector, length r
+    # cross product with iniaxis = [0,0,1]
+    cent = SVector(-cent[2], cent[1])
+    r2 = cent[1]^2 + cent[2]^2
+    du = iniamplitude / (2 * π) * exp(0.5 * (1 - r2)) # vel. perturbation
+    dtemp = -(equations.gamma - 1) / (2 * equations.gamma * rt) * du^2            # isentrop
+    rho = rho * (1 + dtemp)^(1 \ (equations.gamma - 1))
+    vel = vel + du * cent
+    v1, v2 = vel
+    p = p * (1 + dtemp)^(equations.gamma / (equations.gamma - 1))
+    prim = SVector(rho, v1, v2, p)
+    return prim2cons(prim, equations)
 end
 initial_condition = initial_condition_isentropic_vortex
-solver = DGSEM(polydeg=3, surface_flux=flux_lax_friedrichs)
+solver = DGSEM(polydeg = 3, surface_flux = flux_lax_friedrichs)
 
 coordinates_min = (-10.0, -10.0)
-coordinates_max = ( 10.0,  10.0)
-mesh = P4estMesh((1, 1), polydeg=Trixi.polydeg(solver),
-                 coordinates_min=coordinates_min, coordinates_max=coordinates_max,
-                 initial_refinement_level=4)
-
+coordinates_max = (10.0, 10.0)
+mesh = P4estMesh((1, 1), polydeg = Trixi.polydeg(solver),
+                 coordinates_min = coordinates_min, coordinates_max = coordinates_max,
+                 initial_refinement_level = 4)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)
 
@@ -66,19 +65,20 @@ ode = semidiscretize(semi, tspan)
 summary_callback = SummaryCallback()
 
 analysis_interval = 100
-analysis_callback = AnalysisCallback(semi, interval=analysis_interval, save_analysis=true,
-                                     extra_analysis_errors=(:conservation_error,),
-                                     extra_analysis_integrals=(entropy, energy_total,
-                                                               energy_kinetic, energy_internal))
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval,
+                                     save_analysis = true,
+                                     extra_analysis_errors = (:conservation_error,),
+                                     extra_analysis_integrals = (entropy, energy_total,
+                                                                 energy_kinetic,
+                                                                 energy_internal))
 
-alive_callback = AliveCallback(analysis_interval=analysis_interval)
+alive_callback = AliveCallback(analysis_interval = analysis_interval)
 
 callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback)
 
-
 ###############################################################################
 # run the simulation
 
 sol = solve(ode, BS3(),
-            save_everystep=false, callback=callbacks);
+            save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary